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- PDB-9inc: High resolutional Crystal Structure of human H2A.Z-H2B dimer in c... -

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Basic information

Entry
Database: PDB / ID: 9inc
TitleHigh resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z domain
Components
  • Histone H2A.Z
  • Histone H2B type 1-J
  • Vacuolar protein sorting-associated protein 72 homolog
KeywordsNUCLEAR PROTEIN / Histones and its chaperone
Function / homology
Function and homology information


histone chaperone activity / regulation of double-strand break repair / nucleosomal DNA binding / NuA4 histone acetyltransferase complex / somatic stem cell population maintenance / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of double-strand break repair via homologous recombination / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / protein localization to CENP-A containing chromatin ...histone chaperone activity / regulation of double-strand break repair / nucleosomal DNA binding / NuA4 histone acetyltransferase complex / somatic stem cell population maintenance / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of double-strand break repair via homologous recombination / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / transcription initiation-coupled chromatin remodeling / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / cellular response to estradiol stimulus / chromatin DNA binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / antibacterial humoral response / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / heterochromatin formation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Oxidative Stress Induced Senescence / histone binding / regulation of apoptotic process / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / Ub-specific processing proteases / regulation of cell cycle / defense response to Gram-positive bacterium / nuclear speck / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Vps72/YL1, N-terminal / YL1 nuclear protein / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B ...Vps72/YL1, N-terminal / YL1 nuclear protein / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B type 1-J / Histone H2A.Z / Vacuolar protein sorting-associated protein 72 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsTan, W.S. / Liu, Y. / Hong, J.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970669 China
CitationJournal: To Be Published
Title: Structural basis of human histone variant H2AZ recognized by human YL1 providing a conserved structural mechanism
Authors: Tan, W.S. / Liu, Y. / Hong, J.J.
History
DepositionJul 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H2A.Z
B: Histone H2B type 1-J
C: Vacuolar protein sorting-associated protein 72 homolog
D: Histone H2A.Z
E: Histone H2B type 1-J
F: Vacuolar protein sorting-associated protein 72 homolog


Theoretical massNumber of molelcules
Total (without water)61,0226
Polymers61,0226
Non-polymers00
Water2,270126
1
A: Histone H2A.Z
B: Histone H2B type 1-J
C: Vacuolar protein sorting-associated protein 72 homolog


Theoretical massNumber of molelcules
Total (without water)30,5113
Polymers30,5113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-48 kcal/mol
Surface area12110 Å2
MethodPISA
2
D: Histone H2A.Z
E: Histone H2B type 1-J
F: Vacuolar protein sorting-associated protein 72 homolog


Theoretical massNumber of molelcules
Total (without water)30,5113
Polymers30,5113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-52 kcal/mol
Surface area11860 Å2
MethodPISA
3
A: Histone H2A.Z
B: Histone H2B type 1-J
C: Vacuolar protein sorting-associated protein 72 homolog

D: Histone H2A.Z
E: Histone H2B type 1-J
F: Vacuolar protein sorting-associated protein 72 homolog


Theoretical massNumber of molelcules
Total (without water)61,0226
Polymers61,0226
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z+1/21
Buried area20130 Å2
ΔGint-100 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.093, 126.990, 70.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histone H2A.Z / H2A/z


Mass: 10521.134 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AZ1, H2AFZ, H2AZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0C0S5
#2: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 10421.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11, H2BFR, HIST1H2BJ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06899
#3: Protein Vacuolar protein sorting-associated protein 72 homolog / Protein YL-1 / Transcription factor-like 1


Mass: 9567.714 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS72, TCFL1, YL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15906
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 45% PEG200 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.01→85.68 Å / Num. obs: 35203 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 13.1
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 9 % / Rmerge(I) obs: 1.574 / Num. unique obs: 2574 / CC1/2: 0.593 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487_000)refinement
PDB_EXTRACT4.2data extraction
DIALSdata reduction
DIALSdata scaling
PHENIX1.20.1_4487_000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→39.77 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 1696 4.85 %
Rwork0.2195 --
obs0.2214 35003 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3609 0 0 126 3735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.762
X-RAY DIFFRACTIONf_dihedral_angle_d14.8331332
X-RAY DIFFRACTIONf_chiral_restr0.042568
X-RAY DIFFRACTIONf_plane_restr0.007638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.070.45131310.42172729X-RAY DIFFRACTION99
2.07-2.140.39461270.30822750X-RAY DIFFRACTION99
2.14-2.210.28551450.25182740X-RAY DIFFRACTION100
2.21-2.30.44221490.34462623X-RAY DIFFRACTION96
2.3-2.410.23661340.21512782X-RAY DIFFRACTION100
2.41-2.530.2551470.21232781X-RAY DIFFRACTION100
2.53-2.690.27711390.21432756X-RAY DIFFRACTION100
2.69-2.90.28381390.22792780X-RAY DIFFRACTION100
2.9-3.190.25161500.22382792X-RAY DIFFRACTION100
3.19-3.650.24241300.21412807X-RAY DIFFRACTION100
3.65-4.60.23471520.17742821X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.1703 Å / Origin y: -23.0867 Å / Origin z: -8.9141 Å
111213212223313233
T0.234 Å2-0.0168 Å2-0.0254 Å2-0.2425 Å20.0084 Å2--0.1921 Å2
L0.8092 °2-0.3444 °20.1739 °2-1.1706 °2-0.3676 °2--0.8881 °2
S-0.0174 Å °0.1009 Å °0.0844 Å °0.1638 Å °-0.0411 Å °-0.113 Å °-0.0708 Å °0.0904 Å °0.06 Å °
Refinement TLS groupSelection details: all

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